rs1436207

Variant names:

• chr10-50278773-A-T
• rs1436207
• ENST00000395526.9:c.-154+810T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000395526.9(ASAH2):​c.-154+810T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0502 in 152,212 control chromosomes in the GnomAD database, including 551 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.050 (551 hom., cov: 31)
• Consequence: ASAH2 ENST00000395526.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 1 publications found

Genes affected

ASAH2 (HGNC:18860): (N-acylsphingosine amidohydrolase 2) Ceramidases (EC 3.5.1.23), such as ASAH2, catalyze hydrolysis of the N-acyl linkage of ceramide, a second messenger in a variety of cellular events, to produce sphingosine. Sphingosine exerts both mitogenic and apoptosis-inducing activities, and its phosphorylated form functions as an intra- and intercellular second messenger (see MIM 603730) (Mitsutake et al., 2001 [PubMed 11328816]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASAH2	ENST00000395526.9	c.-154+810T>A		intron_variant	Intron 1 of 21	1		ENSP00000378897.3

Frequencies

GnomAD3 genomes AF: 0.0500 AC: 7597 AN: 152092 Hom.: 543 Cov.: 31

Gnomad AFR AF: 0.0831

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0351

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0317

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00923

Gnomad OTH AF: 0.0516

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0502 AC: 7639 AN: 152212 Hom.: 551 Cov.: 31 AF XY: 0.0546 AC XY: 4065 AN XY: 74414

African (AFR) AF: 0.0839 AC: 3483 AN: 41512

American (AMR) AF: 0.0350 AC: 535 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3466

East Asian (EAS) AF: 0.328 AC: 1697 AN: 5178

South Asian (SAS) AF: 0.166 AC: 801 AN: 4818

European-Finnish (FIN) AF: 0.0317 AC: 336 AN: 10614

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00923 AC: 628 AN: 68026

Other (OTH) AF: 0.0543 AC: 115 AN: 2116

Alfa AF: 0.0323 Hom.: 29

Bravo AF: 0.0524

Asia WGS AF: 0.237 AC: 820 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.15
DANN	Benign	0.77
PhyloP100		-1.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1436207; hg19: chr10-52038533;